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<h1 class="epydoc">Source Code for <a href="dadi.Plotting-module.html">Module dadi.Plotting</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Routines for Plotting comparisons between model and data.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">These can serve as inspiration for custom routines for one's own purposes.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">Note that all the plotting is done with pylab. To see additional pylab methods:</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring">"import pylab; help(pylab)". Pylab's many functions are documented at </tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring">http://matplotlib.sourceforge.net/contents.html</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">matplotlib</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pylab</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-comment">#: Custom ticks that label only the lowest and highest bins in an FS plot.</tt> </tt>
<a name="_sfsTickLocator"></a><div id="_sfsTickLocator-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="_sfsTickLocator-toggle" onclick="return toggle('_sfsTickLocator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="dadi.Plotting._sfsTickLocator-class.html">_sfsTickLocator</a><tt class="py-op">(</tt><tt class="py-base-class">matplotlib</tt><tt class="py-op">.</tt><tt class="py-base-class">ticker</tt><tt class="py-op">.</tt><tt class="py-base-class">Locator</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_sfsTickLocator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_sfsTickLocator-expanded"><a name="_sfsTickLocator.__call__"></a><div id="_sfsTickLocator.__call__-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="_sfsTickLocator.__call__-toggle" onclick="return toggle('_sfsTickLocator.__call__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting._sfsTickLocator-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_sfsTickLocator.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_sfsTickLocator.__call__-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">        <tt class="py-docstring">'Return the locations of the ticks'</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">            <tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">.</tt><tt class="py-name">get_view_interval</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">            <tt class="py-name">dmin</tt><tt class="py-op">,</tt> <tt class="py-name">dmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">.</tt><tt class="py-name">get_data_interval</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verify_intervals</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">            <tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viewInterval</tt><tt class="py-op">.</tt><tt class="py-name">get_bounds</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">            <tt class="py-name">dmin</tt><tt class="py-op">,</tt> <tt class="py-name">dmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dataInterval</tt><tt class="py-op">.</tt><tt class="py-name">get_bounds</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-name">tmin</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">dmin</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">        <tt class="py-name">tmax</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt> <tt class="py-name">dmax</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-name">tmin</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-name">tmax</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-comment">#: Custom tick formatter</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable dadi.Plotting._ctf=dadi.Plotting-module.html#_ctf"><a title="dadi.Plotting._ctf" class="py-name" href="#" onclick="return doclink('link-0', '_ctf', 'link-0');">_ctf</a></tt> <tt class="py-op">=</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">ticker</tt><tt class="py-op">.</tt><tt class="py-name">FuncFormatter</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt> <tt class="py-string">'%i'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">-</tt><tt class="py-number">0.4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package dadi=dadi-module.html"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-1', 'dadi', 'link-1');">dadi</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module dadi.Numerics=dadi.Numerics-module.html"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-2', 'Numerics', 'link-2');">Numerics</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Module dadi.Inference=dadi.Inference-module.html"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-3', 'Inference', 'link-3');">Inference</a></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"> </tt>
<a name="plot_1d_fs"></a><div id="plot_1d_fs-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="plot_1d_fs-toggle" onclick="return toggle('plot_1d_fs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_1d_fs">plot_1d_fs</a><tt class="py-op">(</tt><tt class="py-param">fs</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_1d_fs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_1d_fs-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring">    Plot a 1-dimensional frequency spectrum.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-docstring">    fs: 1-dimensional Spectrum</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    Note that all the plotting is done with pylab. To see additional pylab</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">    methods: "import pylab; help(pylab)". Pylab's many functions are documented</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    at http://matplotlib.sourceforge.net/contents.html</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">fig_num</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">        <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">gcf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-name">fig_num</tt><tt class="py-op">,</tt> <tt class="py-name">figsize</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-number">7</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">clear</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">semilogy</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">,</tt> <tt class="py-string">'-ob'</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlim</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.sample_sizes()=dadi.Spectrum_mod.Spectrum-class.html#sample_sizes"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-4', 'sample_sizes', 'link-4');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="plot_1d_comp_multinom"></a><div id="plot_1d_comp_multinom-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="plot_1d_comp_multinom-toggle" onclick="return toggle('plot_1d_comp_multinom');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_1d_comp_multinom">plot_1d_comp_multinom</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">residual</tt><tt class="py-op">=</tt><tt class="py-string">'Anscombe'</tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">                          <tt class="py-param">plot_masked</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_1d_comp_multinom-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_1d_comp_multinom-expanded"><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">    Mulitnomial comparison between 1d model and data.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">    model: 1-dimensional model SFS</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">    data: 1-dimensional data SFS</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">    residual: 'Anscombe' for Anscombe residuals, which are more normally</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">              distributed for Poisson sampling. 'linear' for the linear</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">              residuals, which can be less biased.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    plot_masked: Additionally plots (in open circles) results for points in the </tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">                 model or data that were masked.</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring">    This comparison is multinomial in that it rescales the model to optimally</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">    fit the data.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">    <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-5', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Function dadi.Inference.optimally_scaled_sfs()=dadi.Inference-module.html#optimally_scaled_sfs"><a title="dadi.Inference.optimally_scaled_sfs" class="py-name" href="#" onclick="return doclink('link-6', 'optimally_scaled_sfs', 'link-6');">optimally_scaled_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt id="link-7" class="py-name" targets="Function dadi.Plotting.plot_1d_comp_Poisson()=dadi.Plotting-module.html#plot_1d_comp_Poisson"><a title="dadi.Plotting.plot_1d_comp_Poisson" class="py-name" href="#" onclick="return doclink('link-7', 'plot_1d_comp_Poisson', 'link-7');">plot_1d_comp_Poisson</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">fig_num</tt><tt class="py-op">,</tt> <tt class="py-name">residual</tt><tt class="py-op">,</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">                         <tt class="py-name">plot_masked</tt><tt class="py-op">)</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"> </tt>
<a name="plot_1d_comp_Poisson"></a><div id="plot_1d_comp_Poisson-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="plot_1d_comp_Poisson-toggle" onclick="return toggle('plot_1d_comp_Poisson');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_1d_comp_Poisson">plot_1d_comp_Poisson</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">residual</tt><tt class="py-op">=</tt><tt class="py-string">'Anscombe'</tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">                         <tt class="py-param">plot_masked</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_1d_comp_Poisson-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_1d_comp_Poisson-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt class="py-docstring">    Poisson comparison between 1d model and data.</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">    model: 1-dimensional model SFS</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">    data: 1-dimensional data SFS</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">    residual: 'Anscombe' for Anscombe residuals, which are more normally</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring">              distributed for Poisson sampling. 'linear' for the linear</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">              residuals, which can be less biased.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">    plot_masked: Additionally plots (in open circles) results for points in the </tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-docstring">                 model or data that were masked.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">fig_num</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">gcf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-name">fig_num</tt><tt class="py-op">,</tt> <tt class="py-name">figsize</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-number">7</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.fold()=dadi.Spectrum_mod.Spectrum-class.html#fold"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-8', 'fold', 'link-8');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-9', 'Numerics', 'link-2');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Function dadi.Numerics.intersect_masks()=dadi.Numerics-module.html#intersect_masks"><a title="dadi.Numerics.intersect_masks" class="py-name" href="#" onclick="return doclink('link-10', 'intersect_masks', 'link-10');">intersect_masks</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">semilogy</tt><tt class="py-op">(</tt><tt class="py-name">masked_data</tt><tt class="py-op">,</tt> <tt class="py-string">'-ob'</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">semilogy</tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-string">'-or'</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">plot_masked</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">semilogy</tt><tt class="py-op">(</tt><tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-string">'--ob'</tt><tt class="py-op">,</tt> <tt class="py-name">mfc</tt><tt class="py-op">=</tt><tt class="py-string">'w'</tt><tt class="py-op">,</tt> <tt class="py-name">zorder</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">semilogy</tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-string">'--or'</tt><tt class="py-op">,</tt> <tt class="py-name">mfc</tt><tt class="py-op">=</tt><tt class="py-string">'w'</tt><tt class="py-op">,</tt> <tt class="py-name">zorder</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">sharex</tt> <tt class="py-op">=</tt> <tt class="py-name">ax</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">residual</tt> <tt class="py-op">==</tt> <tt class="py-string">'Anscombe'</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-11', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Function dadi.Inference.Anscombe_Poisson_residual()=dadi.Inference-module.html#Anscombe_Poisson_residual"><a title="dadi.Inference.Anscombe_Poisson_residual" class="py-name" href="#" onclick="return doclink('link-12', 'Anscombe_Poisson_residual', 'link-12');">Anscombe_Poisson_residual</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">residual</tt> <tt class="py-op">==</tt> <tt class="py-string">'linear'</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-13', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Function dadi.Inference.linear_Poisson_residual()=dadi.Inference-module.html#linear_Poisson_residual"><a title="dadi.Inference.linear_Poisson_residual" class="py-name" href="#" onclick="return doclink('link-14', 'linear_Poisson_residual', 'link-14');">linear_Poisson_residual</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown class of residual '%s'."</tt> <tt class="py-op">%</tt> <tt class="py-name">residual</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">,</tt> <tt class="py-string">'-og'</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">plot_masked</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-string">'--og'</tt><tt class="py-op">,</tt> <tt class="py-name">mfc</tt><tt class="py-op">=</tt><tt class="py-string">'w'</tt><tt class="py-op">,</tt> <tt class="py-name">zorder</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlim</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"> </tt>
<a name="plot_single_2d_sfs"></a><div id="plot_single_2d_sfs-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="plot_single_2d_sfs-toggle" onclick="return toggle('plot_single_2d_sfs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_single_2d_sfs">plot_single_2d_sfs</a><tt class="py-op">(</tt><tt class="py-param">sfs</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">ax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">                       <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">extend</tt><tt class="py-op">=</tt><tt class="py-string">'neither'</tt><tt class="py-op">,</tt> <tt class="py-param">colorbar</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_single_2d_sfs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_single_2d_sfs-expanded"><a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-docstring">    Heatmap of single 2d SFS. </tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-docstring">    If vmax is greater than a factor of 10, plot on log scale.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">    sfs: SFS to plot</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-docstring">    vmin: Values in sfs below vmin are masked in plot.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"><tt class="py-docstring">    vmax: Values in sfs above vmax saturate the color spectrum.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-docstring">    ax: Axes object to plot into. If None, the result of pylab.gca() is used.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"><tt class="py-docstring">    extend: Whether the colorbar should have 'extension' arrows. See</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"><tt class="py-docstring">            help(pylab.colorbar) for more details.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line"><tt class="py-docstring">    colorbar: Should we plot a colorbar?</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">gca</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmin</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-name">vmin</tt> <tt class="py-op">=</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">cm</tt><tt class="py-op">.</tt><tt class="py-name">hsv</tt><tt class="py-op">.</tt><tt class="py-name">set_under</tt><tt class="py-op">(</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmax</tt> <tt class="py-op">/</tt> <tt class="py-name">vmin</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">10</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">        <tt class="py-comment"># Under matplotlib 1.0.1, default LogFormatter omits some tick lines.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-comment"># This works more consistently.</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-name">norm</tt> <tt class="py-op">=</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">LogNorm</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-number">1e-3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-number">1e-3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">        <tt class="py-name">format</tt> <tt class="py-op">=</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">ticker</tt><tt class="py-op">.</tt><tt class="py-name">LogFormatterMathtext</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-name">norm</tt> <tt class="py-op">=</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">Normalize</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-number">1e-3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">                                           <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-number">1e-3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">        <tt class="py-name">format</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">    <tt class="py-name">mappable</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">pcolor</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_where</tt><tt class="py-op">(</tt><tt class="py-name">sfs</tt><tt class="py-op">&lt;</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">sfs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">                       <tt class="py-name">cmap</tt><tt class="py-op">=</tt><tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">cm</tt><tt class="py-op">.</tt><tt class="py-name">hsv</tt><tt class="py-op">,</tt> <tt class="py-name">shading</tt><tt class="py-op">=</tt><tt class="py-string">'flat'</tt><tt class="py-op">,</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">                       <tt class="py-name">norm</tt><tt class="py-op">=</tt><tt class="py-name">norm</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">.</tt><tt class="py-name">colorbar</tt><tt class="py-op">(</tt><tt class="py-name">mappable</tt><tt class="py-op">,</tt> <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">extend</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-name">format</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">colorbar</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">        <tt class="py-keyword">del</tt> <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">.</tt><tt class="py-name">axes</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'-k'</tt><tt class="py-op">,</tt> <tt class="py-name">lw</tt><tt class="py-op">=</tt><tt class="py-number">0.2</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'pop0'</tt><tt class="py-op">,</tt><tt class="py-string">'pop1'</tt><tt class="py-op">]</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">horizontalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'left'</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">verticalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'bottom'</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_formatter</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="dadi.Plotting._ctf" class="py-name" href="#" onclick="return doclink('link-15', '_ctf', 'link-0');">_ctf</a></tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_locator</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name" targets="Class dadi.Plotting._sfsTickLocator=dadi.Plotting._sfsTickLocator-class.html"><a title="dadi.Plotting._sfsTickLocator" class="py-name" href="#" onclick="return doclink('link-16', '_sfsTickLocator', 'link-16');">_sfsTickLocator</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">yaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_formatter</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="dadi.Plotting._ctf" class="py-name" href="#" onclick="return doclink('link-17', '_ctf', 'link-0');">_ctf</a></tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">yaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_locator</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="dadi.Plotting._sfsTickLocator" class="py-name" href="#" onclick="return doclink('link-18', '_sfsTickLocator', 'link-16');">_sfsTickLocator</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">tick</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">get_ticklines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">yaxis</tt><tt class="py-op">.</tt><tt class="py-name">get_ticklines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-name">tick</tt><tt class="py-op">.</tt><tt class="py-name">set_visible</tt><tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlim</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_ylim</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line"> </tt>
<a name="plot_2d_resid"></a><div id="plot_2d_resid-def"><a name="L197"></a><tt class="py-lineno">197</tt> <a class="py-toggle" href="#" id="plot_2d_resid-toggle" onclick="return toggle('plot_2d_resid');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_2d_resid">plot_2d_resid</a><tt class="py-op">(</tt><tt class="py-param">resid</tt><tt class="py-op">,</tt> <tt class="py-param">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">ax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">                  <tt class="py-param">extend</tt><tt class="py-op">=</tt><tt class="py-string">'neither'</tt><tt class="py-op">,</tt> <tt class="py-param">colorbar</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_2d_resid-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_2d_resid-expanded"><a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-docstring">    Linear heatmap of 2d residual array.</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-docstring">    sfs: Residual array to plot.</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line"><tt class="py-docstring">    resid_range: Values &gt; resid range or &lt; resid_range saturate the color</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"><tt class="py-docstring">                 spectrum.</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"><tt class="py-docstring">    ax: Axes object to plot into. If None, the result of pylab.gca() is used.</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line"><tt class="py-docstring">    extend: Whether the colorbar should have 'extension' arrows. See</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"><tt class="py-docstring">            help(pylab.colorbar) for more details.</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line"><tt class="py-docstring">    colorbar: Should we plot a colorbar?</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">gca</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line"> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">resid_range</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-name">resid_range</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-name">mappable</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">pcolor</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">,</tt> <tt class="py-name">cmap</tt><tt class="py-op">=</tt><tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">cm</tt><tt class="py-op">.</tt><tt class="py-name">RdBu_r</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-name">resid_range</tt><tt class="py-op">,</tt>  </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">                       <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">resid_range</tt><tt class="py-op">,</tt> <tt class="py-name">shading</tt><tt class="py-op">=</tt><tt class="py-string">'flat'</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">    <tt class="py-name">cbticks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">resid_range</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">resid_range</tt><tt class="py-op">]</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-name">format</tt> <tt class="py-op">=</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">ticker</tt><tt class="py-op">.</tt><tt class="py-name">FormatStrFormatter</tt><tt class="py-op">(</tt><tt class="py-string">'%.2g'</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">.</tt><tt class="py-name">colorbar</tt><tt class="py-op">(</tt><tt class="py-name">mappable</tt><tt class="py-op">,</tt> <tt class="py-name">ticks</tt><tt class="py-op">=</tt><tt class="py-name">cbticks</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-name">format</tt><tt class="py-op">,</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">                       <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">extend</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">colorbar</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt class="py-keyword">del</tt> <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">.</tt><tt class="py-name">axes</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'-k'</tt><tt class="py-op">,</tt> <tt class="py-name">lw</tt><tt class="py-op">=</tt><tt class="py-number">0.2</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'pop0'</tt><tt class="py-op">,</tt><tt class="py-string">'pop1'</tt><tt class="py-op">]</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">horizontalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'left'</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">verticalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'bottom'</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_formatter</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="dadi.Plotting._ctf" class="py-name" href="#" onclick="return doclink('link-19', '_ctf', 'link-0');">_ctf</a></tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_locator</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="dadi.Plotting._sfsTickLocator" class="py-name" href="#" onclick="return doclink('link-20', '_sfsTickLocator', 'link-16');">_sfsTickLocator</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">yaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_formatter</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="dadi.Plotting._ctf" class="py-name" href="#" onclick="return doclink('link-21', '_ctf', 'link-0');">_ctf</a></tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">yaxis</tt><tt class="py-op">.</tt><tt class="py-name">set_major_locator</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="dadi.Plotting._sfsTickLocator" class="py-name" href="#" onclick="return doclink('link-22', '_sfsTickLocator', 'link-16');">_sfsTickLocator</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">tick</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">xaxis</tt><tt class="py-op">.</tt><tt class="py-name">get_ticklines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">yaxis</tt><tt class="py-op">.</tt><tt class="py-name">get_ticklines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">        <tt class="py-name">tick</tt><tt class="py-op">.</tt><tt class="py-name">set_visible</tt><tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlim</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_ylim</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line"> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line"><tt class="py-comment"># Used to determine whether colorbars should have 'extended' arrows</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"><tt id="link-23" class="py-name" targets="Variable dadi.Plotting._extend_mapping=dadi.Plotting-module.html#_extend_mapping"><a title="dadi.Plotting._extend_mapping" class="py-name" href="#" onclick="return doclink('link-23', '_extend_mapping', 'link-23');">_extend_mapping</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-string">'neither'</tt><tt class="py-op">,</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">                   <tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-string">'min'</tt><tt class="py-op">,</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">                   <tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-string">'max'</tt><tt class="py-op">,</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">                   <tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-string">'both'</tt><tt class="py-op">}</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"> </tt>
<a name="plot_2d_comp_multinom"></a><div id="plot_2d_comp_multinom-def"><a name="L253"></a><tt class="py-lineno">253</tt> <a class="py-toggle" href="#" id="plot_2d_comp_multinom-toggle" onclick="return toggle('plot_2d_comp_multinom');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_2d_comp_multinom">plot_2d_comp_multinom</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">                          <tt class="py-param">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">                          <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">residual</tt><tt class="py-op">=</tt><tt class="py-string">'Anscombe'</tt><tt class="py-op">,</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">                          <tt class="py-param">adjust</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_2d_comp_multinom-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_2d_comp_multinom-expanded"><a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-docstring">    Mulitnomial comparison between 2d model and data.</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line"><tt class="py-docstring">    model: 2-dimensional model SFS</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"><tt class="py-docstring">    data: 2-dimensional data SFS</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line"><tt class="py-docstring">    vmin, vmax: Minimum and maximum values plotted for sfs are vmin and</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line"><tt class="py-docstring">                vmax respectively.</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line"><tt class="py-docstring">    resid_range: Residual plot saturates at +- resid_range.</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line"><tt class="py-docstring">    residual: 'Anscombe' for Anscombe residuals, which are more normally</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line"><tt class="py-docstring">              distributed for Poisson sampling. 'linear' for the linear</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line"><tt class="py-docstring">              residuals, which can be less biased.</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line"><tt class="py-docstring">    adjust: Should method use automatic 'subplots_adjust'? For advanced</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line"><tt class="py-docstring">            manipulation of plots, it may be useful to make this False.</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"><tt class="py-docstring">    This comparison is multinomial in that it rescales the model to optimally</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line"><tt class="py-docstring">    fit the data.</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">    <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-24', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="dadi.Inference.optimally_scaled_sfs" class="py-name" href="#" onclick="return doclink('link-25', 'optimally_scaled_sfs', 'link-6');">optimally_scaled_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">    <tt id="link-26" class="py-name" targets="Function dadi.Plotting.plot_2d_comp_Poisson()=dadi.Plotting-module.html#plot_2d_comp_Poisson"><a title="dadi.Plotting.plot_2d_comp_Poisson" class="py-name" href="#" onclick="return doclink('link-26', 'plot_2d_comp_Poisson', 'link-26');">plot_2d_comp_Poisson</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">                         <tt class="py-name">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">resid_range</tt><tt class="py-op">,</tt> <tt class="py-name">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">fig_num</tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">                         <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">residual</tt><tt class="py-op">=</tt><tt class="py-name">residual</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">                         <tt class="py-name">adjust</tt><tt class="py-op">=</tt><tt class="py-name">adjust</tt><tt class="py-op">)</tt> </tt>
</div><a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">     </tt>
<a name="plot_2d_comp_Poisson"></a><div id="plot_2d_comp_Poisson-def"><a name="L285"></a><tt class="py-lineno">285</tt> <a class="py-toggle" href="#" id="plot_2d_comp_Poisson-toggle" onclick="return toggle('plot_2d_comp_Poisson');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_2d_comp_Poisson">plot_2d_comp_Poisson</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">                         <tt class="py-param">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">                         <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">residual</tt><tt class="py-op">=</tt><tt class="py-string">'Anscombe'</tt><tt class="py-op">,</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">                         <tt class="py-param">adjust</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_2d_comp_Poisson-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_2d_comp_Poisson-expanded"><a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"><tt class="py-docstring">    Poisson comparison between 2d model and data.</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line"><tt class="py-docstring">    model: 2-dimensional model SFS</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line"><tt class="py-docstring">    data: 2-dimensional data SFS</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line"><tt class="py-docstring">    vmin, vmax: Minimum and maximum values plotted for sfs are vmin and</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line"><tt class="py-docstring">                vmax respectively.</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line"><tt class="py-docstring">    resid_range: Residual plot saturates at +- resid_range.</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line"><tt class="py-docstring">    residual: 'Anscombe' for Anscombe residuals, which are more normally</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line"><tt class="py-docstring">              distributed for Poisson sampling. 'linear' for the linear</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line"><tt class="py-docstring">              residuals, which can be less biased.</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"><tt class="py-docstring">    adjust: Should method use automatic 'subplots_adjust'? For advanced</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line"><tt class="py-docstring">            manipulation of plots, it may be useful to make this False.</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">        <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-27', 'fold', 'link-8');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">    <tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-28', 'Numerics', 'link-2');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="dadi.Numerics.intersect_masks" class="py-name" href="#" onclick="return doclink('link-29', 'intersect_masks', 'link-10');">intersect_masks</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line"> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">fig_num</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">gcf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-name">fig_num</tt><tt class="py-op">,</tt> <tt class="py-name">figsize</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-number">7</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line"> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">adjust</tt><tt class="py-op">:</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplots_adjust</tt><tt class="py-op">(</tt><tt class="py-name">bottom</tt><tt class="py-op">=</tt><tt class="py-number">0.07</tt><tt class="py-op">,</tt> <tt class="py-name">left</tt><tt class="py-op">=</tt><tt class="py-number">0.07</tt><tt class="py-op">,</tt> <tt class="py-name">top</tt><tt class="py-op">=</tt><tt class="py-number">0.94</tt><tt class="py-op">,</tt> <tt class="py-name">right</tt><tt class="py-op">=</tt><tt class="py-number">0.95</tt><tt class="py-op">,</tt>  </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">                              <tt class="py-name">hspace</tt><tt class="py-op">=</tt><tt class="py-number">0.26</tt><tt class="py-op">,</tt> <tt class="py-name">wspace</tt><tt class="py-op">=</tt><tt class="py-number">0.26</tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">    <tt class="py-name">max_toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">    <tt class="py-name">min_toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">        <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max_toplot</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmin</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">        <tt class="py-name">vmin</tt> <tt class="py-op">=</tt> <tt class="py-name">min_toplot</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">    <tt class="py-name">extend</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="dadi.Plotting._extend_mapping" class="py-name" href="#" onclick="return doclink('link-30', '_extend_mapping', 'link-23');">_extend_mapping</a></tt><tt class="py-op">[</tt><tt class="py-name">vmin</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">min_toplot</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">max_toplot</tt><tt class="py-op">]</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line"> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">        <tt class="py-name">data_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">model_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">resid_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_ids</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'pop_ids must be of length 2.'</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">        <tt class="py-name">data_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">        <tt class="py-name">model_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">            <tt class="py-name">model_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">data_pop_ids</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">model_pop_ids</tt> <tt class="py-op">==</tt> <tt class="py-name">data_pop_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">           <tt class="py-name">resid_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">model_pop_ids</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">            <tt class="py-name">resid_pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">    <tt id="link-31" class="py-name" targets="Function dadi.Plotting.plot_single_2d_sfs()=dadi.Plotting-module.html#plot_single_2d_sfs"><a title="dadi.Plotting.plot_single_2d_sfs" class="py-name" href="#" onclick="return doclink('link-31', 'plot_single_2d_sfs', 'link-31');">plot_single_2d_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_data</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">                       <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">data_pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">colorbar</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">'data'</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line"> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">sharex</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">,</tt> <tt class="py-name">sharey</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">    <tt id="link-32" class="py-name"><a title="dadi.Plotting.plot_single_2d_sfs" class="py-name" href="#" onclick="return doclink('link-32', 'plot_single_2d_sfs', 'link-31');">plot_single_2d_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">                       <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">model_pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">extend</tt> <tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">'model'</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">residual</tt> <tt class="py-op">==</tt> <tt class="py-string">'Anscombe'</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">        <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-33', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="dadi.Inference.Anscombe_Poisson_residual" class="py-name" href="#" onclick="return doclink('link-34', 'Anscombe_Poisson_residual', 'link-12');">Anscombe_Poisson_residual</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt><tt class="py-op">,</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">                                              <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">residual</tt> <tt class="py-op">==</tt> <tt class="py-string">'linear'</tt><tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">        <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-35', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="dadi.Inference.linear_Poisson_residual" class="py-name" href="#" onclick="return doclink('link-36', 'linear_Poisson_residual', 'link-14');">linear_Poisson_residual</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt><tt class="py-op">,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">                                            <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown class of residual '%s'."</tt> <tt class="py-op">%</tt> <tt class="py-name">residual</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line"> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">resid_range</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">        <tt class="py-name">resid_range</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">    <tt class="py-name">resid_extend</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="dadi.Plotting._extend_mapping" class="py-name" href="#" onclick="return doclink('link-37', '_extend_mapping', 'link-23');">_extend_mapping</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">resid_range</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">                                   <tt class="py-name">resid_range</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line"> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">    <tt class="py-name">ax3</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-name">sharex</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">,</tt> <tt class="py-name">sharey</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">    <tt id="link-38" class="py-name" targets="Function dadi.Plotting.plot_2d_resid()=dadi.Plotting-module.html#plot_2d_resid"><a title="dadi.Plotting.plot_2d_resid" class="py-name" href="#" onclick="return doclink('link-38', 'plot_2d_resid', 'link-38');">plot_2d_resid</a></tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">,</tt> <tt class="py-name">resid_range</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">resid_pop_ids</tt><tt class="py-op">,</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">                  <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">resid_extend</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">    <tt class="py-name">ax3</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">'residuals'</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line"> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">)</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">    <tt class="py-name">flatresid</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">compress</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_not</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">                               <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">hist</tt><tt class="py-op">(</tt><tt class="py-name">flatresid</tt><tt class="py-op">,</tt> <tt class="py-name">bins</tt><tt class="py-op">=</tt><tt class="py-number">20</tt><tt class="py-op">,</tt> <tt class="py-name">normed</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">'residuals'</tt><tt class="py-op">)</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_yticks</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line"> </tt>
<a name="plot_3d_comp_multinom"></a><div id="plot_3d_comp_multinom-def"><a name="L382"></a><tt class="py-lineno">382</tt> <a class="py-toggle" href="#" id="plot_3d_comp_multinom-toggle" onclick="return toggle('plot_3d_comp_multinom');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_3d_comp_multinom">plot_3d_comp_multinom</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">                          <tt class="py-param">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">                          <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">residual</tt><tt class="py-op">=</tt><tt class="py-string">'Anscombe'</tt><tt class="py-op">,</tt> <tt class="py-param">adjust</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_3d_comp_multinom-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_3d_comp_multinom-expanded"><a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line"><tt class="py-docstring">    Multinomial comparison between 3d model and data.</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line"><tt class="py-docstring">    model: 3-dimensional model SFS</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line"><tt class="py-docstring">    data: 3-dimensional data SFS</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line"><tt class="py-docstring">    vmin, vmax: Minimum and maximum values plotted for sfs are vmin and</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line"><tt class="py-docstring">                vmax respectively.</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line"><tt class="py-docstring">    resid_range: Residual plot saturates at +- resid_range.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line"><tt class="py-docstring">    residual: 'Anscombe' for Anscombe residuals, which are more normally</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line"><tt class="py-docstring">              distributed for Poisson sampling. 'linear' for the linear</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line"><tt class="py-docstring">              residuals, which can be less biased.</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"><tt class="py-docstring">    adjust: Should method use automatic 'subplots_adjust'? For advanced</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"><tt class="py-docstring">            manipulation of plots, it may be useful to make this False.</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line"><tt class="py-docstring">    This comparison is multinomial in that it rescales the model to optimally</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-docstring">    fit the data.</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">    <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-39', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="dadi.Inference.optimally_scaled_sfs" class="py-name" href="#" onclick="return doclink('link-40', 'optimally_scaled_sfs', 'link-6');">optimally_scaled_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line"> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">    <tt id="link-41" class="py-name" targets="Function dadi.Plotting.plot_3d_comp_Poisson()=dadi.Plotting-module.html#plot_3d_comp_Poisson"><a title="dadi.Plotting.plot_3d_comp_Poisson" class="py-name" href="#" onclick="return doclink('link-41', 'plot_3d_comp_Poisson', 'link-41');">plot_3d_comp_Poisson</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">                         <tt class="py-name">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">resid_range</tt><tt class="py-op">,</tt> <tt class="py-name">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">fig_num</tt><tt class="py-op">,</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">                         <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">residual</tt><tt class="py-op">=</tt><tt class="py-name">residual</tt><tt class="py-op">,</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">                         <tt class="py-name">adjust</tt><tt class="py-op">=</tt><tt class="py-name">adjust</tt><tt class="py-op">)</tt> </tt>
</div><a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line"> </tt>
<a name="plot_3d_comp_Poisson"></a><div id="plot_3d_comp_Poisson-def"><a name="L413"></a><tt class="py-lineno">413</tt> <a class="py-toggle" href="#" id="plot_3d_comp_Poisson-toggle" onclick="return toggle('plot_3d_comp_Poisson');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_3d_comp_Poisson">plot_3d_comp_Poisson</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">                         <tt class="py-param">resid_range</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">fig_num</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">                         <tt class="py-param">residual</tt><tt class="py-op">=</tt><tt class="py-string">'Anscombe'</tt><tt class="py-op">,</tt> <tt class="py-param">adjust</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_3d_comp_Poisson-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_3d_comp_Poisson-expanded"><a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line"><tt class="py-docstring">    Poisson comparison between 3d model and data.</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line"><tt class="py-docstring">    model: 3-dimensional model SFS</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line"><tt class="py-docstring">    data: 3-dimensional data SFS</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line"><tt class="py-docstring">    vmin, vmax: Minimum and maximum values plotted for sfs are vmin and</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line"><tt class="py-docstring">                vmax respectively.</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line"><tt class="py-docstring">    resid_range: Residual plot saturates at +- resid_range.</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line"><tt class="py-docstring">    fig_num: Clear and use figure fig_num for display. If None, an new figure</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line"><tt class="py-docstring">             window is created.</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line"><tt class="py-docstring">    residual: 'Anscombe' for Anscombe residuals, which are more normally</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line"><tt class="py-docstring">              distributed for Poisson sampling. 'linear' for the linear</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line"><tt class="py-docstring">              residuals, which can be less biased.</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt>  <tt class="py-line"><tt class="py-docstring">    adjust: Should method use automatic 'subplots_adjust'? For advanced</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line"><tt class="py-docstring">            manipulation of plots, it may be useful to make this False.</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">        <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-42', 'fold', 'link-8');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line"> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">    <tt class="py-name">masked_model</tt><tt class="py-op">,</tt> <tt class="py-name">masked_data</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-43', 'Numerics', 'link-2');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="dadi.Numerics.intersect_masks" class="py-name" href="#" onclick="return doclink('link-44', 'intersect_masks', 'link-10');">intersect_masks</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line"> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">fig_num</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">gcf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-name">fig_num</tt><tt class="py-op">,</tt> <tt class="py-name">figsize</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">,</tt><tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line"> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">adjust</tt><tt class="py-op">:</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplots_adjust</tt><tt class="py-op">(</tt><tt class="py-name">bottom</tt><tt class="py-op">=</tt><tt class="py-number">0.07</tt><tt class="py-op">,</tt> <tt class="py-name">left</tt><tt class="py-op">=</tt><tt class="py-number">0.07</tt><tt class="py-op">,</tt> <tt class="py-name">top</tt><tt class="py-op">=</tt><tt class="py-number">0.95</tt><tt class="py-op">,</tt> <tt class="py-name">right</tt><tt class="py-op">=</tt><tt class="py-number">0.95</tt><tt class="py-op">)</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line"> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line">    <tt class="py-name">modelmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">    <tt class="py-name">datamax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line">    <tt class="py-name">modelmin</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line">    <tt class="py-name">datamin</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line">    <tt class="py-name">max_toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">modelmax</tt><tt class="py-op">,</tt> <tt class="py-name">datamax</tt><tt class="py-op">)</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">    <tt class="py-name">min_toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">modelmin</tt><tt class="py-op">,</tt> <tt class="py-name">datamin</tt><tt class="py-op">)</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line"> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line">        <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max_toplot</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmin</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line">        <tt class="py-name">vmin</tt> <tt class="py-op">=</tt> <tt class="py-name">min_toplot</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line">    <tt class="py-name">extend</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="dadi.Plotting._extend_mapping" class="py-name" href="#" onclick="return doclink('link-45', '_extend_mapping', 'link-23');">_extend_mapping</a></tt><tt class="py-op">[</tt><tt class="py-name">vmin</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">min_toplot</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">max_toplot</tt><tt class="py-op">]</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line"> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line">    <tt class="py-comment"># Calculate the residuals</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">residual</tt> <tt class="py-op">==</tt> <tt class="py-string">'Anscombe'</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">        <tt class="py-name">resids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-46', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt>\ </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line">                  <tt id="link-47" class="py-name"><a title="dadi.Inference.Anscombe_Poisson_residual" class="py-name" href="#" onclick="return doclink('link-47', 'Anscombe_Poisson_residual', 'link-12');">Anscombe_Poisson_residual</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line">                                            <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">                                            <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">residual</tt> <tt class="py-op">==</tt> <tt class="py-string">'linear'</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line">        <tt class="py-name">resids</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-48', 'Inference', 'link-3');">Inference</a></tt><tt class="py-op">.</tt>\ </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line">                 <tt id="link-49" class="py-name"><a title="dadi.Inference.linear_Poisson_residual" class="py-name" href="#" onclick="return doclink('link-49', 'linear_Poisson_residual', 'link-14');">linear_Poisson_residual</a></tt><tt class="py-op">(</tt><tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">                                         <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line">                                         <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown class of residual '%s'."</tt> <tt class="py-op">%</tt> <tt class="py-name">residual</tt><tt class="py-op">)</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt>  <tt class="py-line"> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line"> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line">    <tt class="py-name">min_resid</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">resids</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line">    <tt class="py-name">max_resid</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">resids</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">resid_range</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">        <tt class="py-name">resid_range</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">max_resid</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">min_resid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">    <tt class="py-name">resid_extend</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="dadi.Plotting._extend_mapping" class="py-name" href="#" onclick="return doclink('link-50', '_extend_mapping', 'link-23');">_extend_mapping</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">resid_range</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">min_resid</tt><tt class="py-op">,</tt>  </tt>
<a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">                                   <tt class="py-name">resid_range</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">max_resid</tt><tt class="py-op">]</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line"> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'pop_ids must be of length 3.'</tt><tt class="py-op">)</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line">        <tt class="py-name">data_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">model_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">resid_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_ids</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line">        <tt class="py-name">data_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line">        <tt class="py-name">model_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line"> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">model_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">            <tt class="py-name">model_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">data_ids</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line"> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">model_ids</tt> <tt class="py-op">==</tt> <tt class="py-name">data_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt>  <tt class="py-line">           <tt class="py-name">resid_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">model_ids</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line">            <tt class="py-name">resid_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt>  <tt class="py-line"> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">sax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line">        <tt class="py-name">marg_data</tt> <tt class="py-op">=</tt> <tt class="py-name">masked_data</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt>  <tt class="py-line">        <tt class="py-name">marg_model</tt> <tt class="py-op">=</tt> <tt class="py-name">masked_model</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt>  <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line">        <tt class="py-name">curr_ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ids</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">data_ids</tt><tt class="py-op">,</tt> <tt class="py-name">model_ids</tt><tt class="py-op">,</tt> <tt class="py-name">resid_ids</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line">                <tt class="py-name">ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'pop0'</tt><tt class="py-op">,</tt> <tt class="py-string">'pop1'</tt><tt class="py-op">,</tt> <tt class="py-string">'pop2'</tt><tt class="py-op">]</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line"> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt>  <tt class="py-line">                <tt class="py-name">ids</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">ids</tt><tt class="py-op">)</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line">                <tt class="py-keyword">del</tt> <tt class="py-name">ids</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">-</tt><tt class="py-name">sax</tt><tt class="py-op">]</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt>  <tt class="py-line"> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt>  <tt class="py-line">            <tt class="py-name">curr_ids</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">ids</tt><tt class="py-op">)</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt>  <tt class="py-line"> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-name">sax</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt>  <tt class="py-line">        <tt class="py-name">plot_colorbar</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">sax</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line">        <tt id="link-51" class="py-name"><a title="dadi.Plotting.plot_single_2d_sfs" class="py-name" href="#" onclick="return doclink('link-51', 'plot_single_2d_sfs', 'link-31');">plot_single_2d_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">marg_data</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">curr_ids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt>  <tt class="py-line">                           <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">extend</tt><tt class="py-op">,</tt> <tt class="py-name">colorbar</tt><tt class="py-op">=</tt><tt class="py-name">plot_colorbar</tt><tt class="py-op">)</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line"> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-name">sax</tt><tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-name">sharex</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">,</tt> <tt class="py-name">sharey</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">)</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt>  <tt class="py-line">        <tt id="link-52" class="py-name"><a title="dadi.Plotting.plot_single_2d_sfs" class="py-name" href="#" onclick="return doclink('link-52', 'plot_single_2d_sfs', 'link-31');">plot_single_2d_sfs</a></tt><tt class="py-op">(</tt><tt class="py-name">marg_model</tt><tt class="py-op">,</tt> <tt class="py-name">vmin</tt><tt class="py-op">=</tt><tt class="py-name">vmin</tt><tt class="py-op">,</tt> <tt class="py-name">vmax</tt><tt class="py-op">=</tt><tt class="py-name">vmax</tt><tt class="py-op">,</tt>  </tt>
<a name="L521"></a><tt class="py-lineno">521</tt>  <tt class="py-line">                           <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">curr_ids</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">extend</tt><tt class="py-op">,</tt> <tt class="py-name">colorbar</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt>  <tt class="py-line"> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt>  <tt class="py-line">        <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt class="py-name">resids</tt><tt class="py-op">[</tt><tt class="py-name">sax</tt><tt class="py-op">]</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line">        <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-name">sax</tt><tt class="py-op">+</tt><tt class="py-number">7</tt><tt class="py-op">,</tt> <tt class="py-name">sharex</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">,</tt> <tt class="py-name">sharey</tt><tt class="py-op">=</tt><tt class="py-name">ax</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line">        <tt id="link-53" class="py-name"><a title="dadi.Plotting.plot_2d_resid" class="py-name" href="#" onclick="return doclink('link-53', 'plot_2d_resid', 'link-38');">plot_2d_resid</a></tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">,</tt> <tt class="py-name">resid_range</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">curr_ids</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt>  <tt class="py-line">                      <tt class="py-name">extend</tt><tt class="py-op">=</tt><tt class="py-name">resid_extend</tt><tt class="py-op">,</tt> <tt class="py-name">colorbar</tt><tt class="py-op">=</tt><tt class="py-name">plot_colorbar</tt><tt class="py-op">)</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt>  <tt class="py-line"> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-name">sax</tt><tt class="py-op">+</tt><tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt>  <tt class="py-line">        <tt class="py-name">flatresid</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">compress</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_not</tt><tt class="py-op">(</tt><tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line">                                   <tt class="py-name">resid</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">hist</tt><tt class="py-op">(</tt><tt class="py-name">flatresid</tt><tt class="py-op">,</tt> <tt class="py-name">bins</tt><tt class="py-op">=</tt><tt class="py-number">20</tt><tt class="py-op">,</tt> <tt class="py-name">normed</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_yticks</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line"> </tt>
<a name="plot_3d_spectrum"></a><div id="plot_3d_spectrum-def"><a name="L535"></a><tt class="py-lineno">535</tt> <a class="py-toggle" href="#" id="plot_3d_spectrum-toggle" onclick="return toggle('plot_3d_spectrum');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_3d_spectrum">plot_3d_spectrum</a><tt class="py-op">(</tt><tt class="py-param">fs</tt><tt class="py-op">,</tt> <tt class="py-param">fignum</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_3d_spectrum-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_3d_spectrum-expanded"><a name="L536"></a><tt class="py-lineno">536</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt>  <tt class="py-line"><tt class="py-docstring">    Logarithmic heatmap of single 3d FS.</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line"><tt class="py-docstring">    Note that this method is slow, because it relies on matplotlib's software</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt>  <tt class="py-line"><tt class="py-docstring">    rendering. For faster and better looking plots, use plot_3d_spectrum_mayavi.</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line"><tt class="py-docstring">    fs: FS to plot</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt>  <tt class="py-line"><tt class="py-docstring">    vmin: Values in fs below vmin are masked in plot.</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line"><tt class="py-docstring">    vmax: Values in fs above vmax saturate the color spectrum.</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt>  <tt class="py-line"><tt class="py-docstring">    fignum: Figure number to plot into. If None, a new figure will be created.</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">mpl_toolkits</tt><tt class="py-op">.</tt><tt class="py-name">mplot3d</tt> <tt class="py-keyword">as</tt> <tt class="py-name">mplot3d</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt>  <tt class="py-line">     </tt>
<a name="L550"></a><tt class="py-lineno">550</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-name">fignum</tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">mplot3d</tt><tt class="py-op">.</tt><tt class="py-name">Axes3D</tt><tt class="py-op">(</tt><tt class="py-name">fig</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line"> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmin</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt>  <tt class="py-line">        <tt class="py-name">vmin</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line">        <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line"> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">    <tt class="py-comment"># Which entries should I plot?</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt>  <tt class="py-line">    <tt class="py-name">toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_not</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">)</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line">    <tt class="py-name">toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_and</tt><tt class="py-op">(</tt><tt class="py-name">toplot</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">vmin</tt><tt class="py-op">)</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt>  <tt class="py-line">     </tt>
<a name="L562"></a><tt class="py-lineno">562</tt>  <tt class="py-line">    <tt class="py-comment"># Figure out the color mapping.</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt>  <tt class="py-line">    <tt class="py-name">normalized</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>\ </tt>
<a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line">            <tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">vmax</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line">    <tt class="py-name">normalized</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">normalized</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line">    <tt class="py-name">colors</tt> <tt class="py-op">=</tt> <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">cm</tt><tt class="py-op">.</tt><tt class="py-name">hsv</tt><tt class="py-op">(</tt><tt class="py-name">normalized</tt><tt class="py-op">)</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line">     </tt>
<a name="L568"></a><tt class="py-lineno">568</tt>  <tt class="py-line">    <tt class="py-comment"># We draw by calculating which faces are visible and including each as a</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt>  <tt class="py-line">    <tt class="py-comment"># polygon.</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt>  <tt class="py-line">    <tt class="py-name">polys</tt><tt class="py-op">,</tt> <tt class="py-name">polycolors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">kk</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt>  <tt class="py-line">                    <tt class="py-keyword">pass</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt>  <tt class="py-line">                    <tt class="py-name">polys</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt>  <tt class="py-line">                                  <tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt>  <tt class="py-line">                    <tt class="py-name">polycolors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">kk</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt>  <tt class="py-line">                    <tt class="py-keyword">pass</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt>  <tt class="py-line">                    <tt class="py-name">polys</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt>  <tt class="py-line">                                  <tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt>  <tt class="py-line">                    <tt class="py-name">polycolors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">jj</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt>  <tt class="py-line">                    <tt class="py-keyword">pass</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt>  <tt class="py-line">                    <tt class="py-name">polys</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt>  <tt class="py-line">                                  <tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt>  <tt class="py-line">                    <tt class="py-name">polycolors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">jj</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt>  <tt class="py-line">                    <tt class="py-keyword">pass</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt>  <tt class="py-line">                    <tt class="py-name">polys</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt>  <tt class="py-line">                                  <tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt>  <tt class="py-line">                    <tt class="py-name">polycolors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">ii</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt>  <tt class="py-line">                    <tt class="py-keyword">pass</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt>  <tt class="py-line">                    <tt class="py-name">polys</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt>  <tt class="py-line">                                  <tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt>  <tt class="py-line">                    <tt class="py-name">polycolors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">ii</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">toplot</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt>  <tt class="py-line">                    <tt class="py-keyword">pass</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt>  <tt class="py-line">                    <tt class="py-name">polys</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt>  <tt class="py-line">                                  <tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt>  <tt class="py-line">                                 <tt class="py-op">)</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt>  <tt class="py-line">                    <tt class="py-name">polycolors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt>  <tt class="py-line">                     </tt>
<a name="L619"></a><tt class="py-lineno">619</tt>  <tt class="py-line"> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt>  <tt class="py-line">    <tt class="py-name">polycoll</tt> <tt class="py-op">=</tt> <tt class="py-name">mplot3d</tt><tt class="py-op">.</tt><tt class="py-name">art3d</tt><tt class="py-op">.</tt><tt class="py-name">Poly3DCollection</tt><tt class="py-op">(</tt><tt class="py-name">polys</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">polycolors</tt><tt class="py-op">,</tt>  </tt>
<a name="L621"></a><tt class="py-lineno">621</tt>  <tt class="py-line">                                              <tt class="py-name">edgecolor</tt><tt class="py-op">=</tt><tt class="py-string">'k'</tt><tt class="py-op">,</tt> <tt class="py-name">linewidths</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">add_collection</tt><tt class="py-op">(</tt><tt class="py-name">polycoll</tt><tt class="py-op">)</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt>  <tt class="py-line"> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt>  <tt class="py-line">    <tt class="py-comment"># Set the limits</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlim3d</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_ylim3d</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_zlim3d</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt>  <tt class="py-line"> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'pop0'</tt><tt class="py-op">,</tt><tt class="py-string">'pop1'</tt><tt class="py-op">,</tt><tt class="py-string">'pop2'</tt><tt class="py-op">]</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">horizontalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'left'</tt><tt class="py-op">)</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">verticalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'bottom'</tt><tt class="py-op">)</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">set_zlabel</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">verticalalignment</tt><tt class="py-op">=</tt><tt class="py-string">'bottom'</tt><tt class="py-op">)</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt>  <tt class="py-line"> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt>  <tt class="py-line">    <tt class="py-comment"># XXX: I can't set the axis ticks to be just the endpoints.</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt>  <tt class="py-line"> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt>  <tt class="py-line">    <tt class="py-name">pylab</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L641"></a><tt class="py-lineno">641</tt>  <tt class="py-line"> </tt>
<a name="plot_3d_spectrum_mayavi"></a><div id="plot_3d_spectrum_mayavi-def"><a name="L642"></a><tt class="py-lineno">642</tt> <a class="py-toggle" href="#" id="plot_3d_spectrum_mayavi-toggle" onclick="return toggle('plot_3d_spectrum_mayavi');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Plotting-module.html#plot_3d_spectrum_mayavi">plot_3d_spectrum_mayavi</a><tt class="py-op">(</tt><tt class="py-param">fs</tt><tt class="py-op">,</tt> <tt class="py-param">fignum</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmin</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">vmax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  </tt>
<a name="L643"></a><tt class="py-lineno">643</tt>  <tt class="py-line">                            <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_3d_spectrum_mayavi-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_3d_spectrum_mayavi-expanded"><a name="L644"></a><tt class="py-lineno">644</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt>  <tt class="py-line"><tt class="py-docstring">    Logarithmic heatmap of single 3d FS.</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt>  <tt class="py-line"><tt class="py-docstring">    This method relies on MayaVi2's mlab interface. See http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/mlab.html . To edit plot</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt>  <tt class="py-line"><tt class="py-docstring">    properties, click leftmost icon in the toolbar.</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt>  <tt class="py-line"><tt class="py-docstring">    If you get an ImportError upon calling this function, it is likely that you</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt>  <tt class="py-line"><tt class="py-docstring">    don't have mayavi installed.</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt>  <tt class="py-line"><tt class="py-docstring">    fs: FS to plot</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt>  <tt class="py-line"><tt class="py-docstring">    vmin: Values in fs below vmin are masked in plot.</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt>  <tt class="py-line"><tt class="py-docstring">    vmax: Values in fs above vmax saturate the color spectrum.</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt>  <tt class="py-line"><tt class="py-docstring">    fignum: Figure number to plot into. If None, a new figure will be created.</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt>  <tt class="py-line"><tt class="py-docstring">            Note that these are MayaVi figures, which are separate from</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt>  <tt class="py-line"><tt class="py-docstring">            matplotlib figures.</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt>  <tt class="py-line"><tt class="py-docstring">    pop_ids: If not None, override pop_ids stored in Spectrum.</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">enthought</tt><tt class="py-op">.</tt><tt class="py-name">mayavi</tt> <tt class="py-keyword">import</tt> <tt class="py-name">mlab</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt>  <tt class="py-line"> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-name">fignum</tt><tt class="py-op">,</tt> <tt class="py-name">bgcolor</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt>  <tt class="py-line">    <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-name">fig</tt><tt class="py-op">)</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt>  <tt class="py-line"> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmin</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt>  <tt class="py-line">        <tt class="py-name">vmin</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">vmax</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt>  <tt class="py-line">        <tt class="py-name">vmax</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt>  <tt class="py-line"> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt>  <tt class="py-line">    <tt class="py-comment"># Which entries should I plot?</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt>  <tt class="py-line">    <tt class="py-name">toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_not</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">)</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt>  <tt class="py-line">    <tt class="py-name">toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_and</tt><tt class="py-op">(</tt><tt class="py-name">toplot</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">vmin</tt><tt class="py-op">)</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt>  <tt class="py-line"> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt>  <tt class="py-line">    <tt class="py-comment"># For the color mapping</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt>  <tt class="py-line">    <tt class="py-name">normalized</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>\ </tt>
<a name="L677"></a><tt class="py-lineno">677</tt>  <tt class="py-line">            <tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">vmax</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">vmin</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt>  <tt class="py-line">    <tt class="py-name">normalized</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">normalized</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt>  <tt class="py-line"> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt>  <tt class="py-line">    <tt class="py-name">xs</tt><tt class="py-op">,</tt><tt class="py-name">ys</tt><tt class="py-op">,</tt><tt class="py-name">zs</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">indices</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt>  <tt class="py-line">    <tt class="py-name">flat_xs</tt> <tt class="py-op">=</tt> <tt class="py-name">xs</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt>  <tt class="py-line">    <tt class="py-name">flat_ys</tt> <tt class="py-op">=</tt> <tt class="py-name">ys</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt>  <tt class="py-line">    <tt class="py-name">flat_zs</tt> <tt class="py-op">=</tt> <tt class="py-name">zs</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt>  <tt class="py-line">    <tt class="py-name">flat_toplot</tt> <tt class="py-op">=</tt> <tt class="py-name">toplot</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt>  <tt class="py-line">     </tt>
<a name="L686"></a><tt class="py-lineno">686</tt>  <tt class="py-line">    <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">barchart</tt><tt class="py-op">(</tt><tt class="py-name">flat_xs</tt><tt class="py-op">[</tt><tt class="py-name">flat_toplot</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">flat_ys</tt><tt class="py-op">[</tt><tt class="py-name">flat_toplot</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L687"></a><tt class="py-lineno">687</tt>  <tt class="py-line">                  <tt class="py-name">flat_zs</tt><tt class="py-op">[</tt><tt class="py-name">flat_toplot</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">normalized</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">flat_toplot</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L688"></a><tt class="py-lineno">688</tt>  <tt class="py-line">                  <tt class="py-name">colormap</tt><tt class="py-op">=</tt><tt class="py-string">'hsv'</tt><tt class="py-op">,</tt> <tt class="py-name">scale_mode</tt><tt class="py-op">=</tt><tt class="py-string">'none'</tt><tt class="py-op">,</tt> <tt class="py-name">lateral_scale</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt>  </tt>
<a name="L689"></a><tt class="py-lineno">689</tt>  <tt class="py-line">                  <tt class="py-name">figure</tt><tt class="py-op">=</tt><tt class="py-name">fig</tt><tt class="py-op">)</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt>  <tt class="py-line"> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'pop0'</tt><tt class="py-op">,</tt><tt class="py-string">'pop1'</tt><tt class="py-op">,</tt><tt class="py-string">'pop2'</tt><tt class="py-op">]</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt>  <tt class="py-line"> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt>  <tt class="py-line">    <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">axes</tt><tt class="py-op">(</tt><tt class="py-name">xlabel</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">ylabel</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">zlabel</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L698"></a><tt class="py-lineno">698</tt>  <tt class="py-line">                  <tt class="py-name">figure</tt><tt class="py-op">=</tt><tt class="py-name">fig</tt><tt class="py-op">,</tt> <tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt>  <tt class="py-line">    <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">axes</tt><tt class="py-op">.</tt><tt class="py-name">label_format</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt>  <tt class="py-line">    <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">title_text_property</tt><tt class="py-op">.</tt><tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt>  <tt class="py-line">    <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">text3d</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-54', 'sample_sizes', 'link-4');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-55', 'sample_sizes', 'link-4');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-56', 'sample_sizes', 'link-4');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt>  </tt>
<a name="L702"></a><tt class="py-lineno">702</tt>  <tt class="py-line">                <tt class="py-string">'(%i,%i,%i)'</tt><tt class="py-op">%</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-57', 'sample_sizes', 'link-4');">sample_sizes</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">scale</tt><tt class="py-op">=</tt><tt class="py-number">0.75</tt><tt class="py-op">,</tt> <tt class="py-name">figure</tt><tt class="py-op">=</tt><tt class="py-name">fig</tt><tt class="py-op">,</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt>  <tt class="py-line">                <tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt>  <tt class="py-line">    <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-name">azimuth</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">40</tt><tt class="py-op">,</tt> <tt class="py-name">elevation</tt><tt class="py-op">=</tt><tt class="py-number">65</tt><tt class="py-op">,</tt> <tt class="py-name">distance</tt><tt class="py-op">=</tt><tt class="py-string">'auto'</tt><tt class="py-op">,</tt> <tt class="py-name">focalpoint</tt><tt class="py-op">=</tt><tt class="py-string">'auto'</tt><tt class="py-op">)</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt>  <tt class="py-line"> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt>  <tt class="py-line">    <tt class="py-name">mlab</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L707"></a><tt class="py-lineno">707</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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